AEG's Swashbuckling Adventures offers some great classes, prestige classes and feats for pirates and swashbucklers. Granted, the classes (and feats, for that matter) are for the most part overpowered and require adjustments for 3.5e, but it helped form the basis of my recent swashbuckler campaign.
Classes (20 levels) that might prove useful include:
Musketeer - Elegant duelists in service to the crown
Noble - Charismatic aristocrats
Pirate - Arrrr! (Speaks for itself. Way too powerful, though.)
Spy - Specialized rogue
Swashbuckler - Before Complete Warrior there was Swashbuckling Adventures
Wanderer - Expert for PCs, with a gift for self-preservation
Prestige Classes (5 levels, unless otherwise noted):
Boarding Marine (10 levels) - Never board a ship without 'em
Buccaneer (10 levels) - Pirate brotherhood with benefits for fighting together
Captain - Tactics oriented and...fairly useless.
Daring Fool (10 levels) - Risk-taking, daredeviling, swashbuckling roguish types
Entertainment Officer - All a-bard! (sorry)
Field Surgeon - For those who can't afford magical healing
Helmsman - Good for an NPC who steers the ship
Man of Will (3 levels) - An unstoppable force of inner strength
Master Gunner - Deadly with a cannon
Midshipman - Jack-of-all-trades aboard ship
Naval Marine (10 levels) - Might as well be called Naval Gunslinger
Rogers Swordsman - Gifted sailor with fun pirate tricks and bonus feats
Ship's Chaplain (10 levels) - Cleric of the sea (now chunkier than ever!)
Topman (10 levels) - Specializes in working (as well as fighting in) the rigging
Just to name a few. Granted, most of these are created around the campaign world of Theah, which is included in the book as well. It's a relatively low-magic world based on 17th century Europe (flintlocks and cannons are common). Many of the prestige classes not listed above are focused on regional fighting styles, but can easily be adapted to any culture in one's own setting.